Hi Bill
I mean to pick this up earlier in the week but somehow it slipped
through my net. Sorry.
Anyhows: pack_c.c and pack_f.f are not programs but essentially
subroutine libraries. You would need to write your own program to
actually use them (I'm not sure that there's any documentation btw...)
Hi James,
On the gathering of the data from all possible beamline / source /
detector combinations below, I am also keen to get hold of these. To
assist with this I have written a couple of bash shell scripts which
will tar, gzip and split into 128MB chunks data, then reverse this
process to ensu
Hi James,
The old mar345 images were compressed with the "pack" which Bill is
referring to. This is suppoprted in CBFlib.
PNG and jpeg2000 may well do "better" at compression (would like to see
the numbers with this) but are likely to be much slower than something
customised for use with diffract
Hi
Lossy compression should be okay, provided that the errors introduced are
smaller than those expected for counting statistics (assuming that the
pixels are more-or-less independent) - i.e. less than the square-root of
the individual pixel intensities (though I don't see why this can't be
e
Dear all,
I think we need to stop and think right here. The errors in pixel
values of images are neither Poisson (i.e. forget about taking square roots)
nor independent. Our ideas about image statistics are already disastrously
poor enough: the last thing we need is to make matters even worse
Dear All,
there was a paper (quite) a while ago where someone made
for the first time a racemic protein mixture, obtained a
centrosymmetric structure and solved it (not the 2003
PNAS paper by the Eisenberg grp).
Hints appreciated.
Thx, br
oopss...Not science:
Proteins: Structure, Function, and Genetics
Volume 16, Issue 3 , Pages 301 - 305 (1993)
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Soisson, Stephen Michael
Sent: Friday, August 24, 2007 10:59 AM
To: CCP4BB@JISCMAIL.AC.UK
Subj
Wow.
I don't know about the rest of you, but I got told three times.
Gerard is, of course, right about pixel non-independence (think "point
spread function", among other things), and I wouldn't care to argue
statistics with him, but as far as I know (and I could well be wrong) most
of the in
Jeremy Berg, Rubredoxin. In Science around 1995.
Steve
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Bernhard Rupp
Sent: Friday, August 24, 2007 10:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] centrosymm structure
Dear All,
there was a paper (
Two postdoctoral positions are available immediately to study
structure-function relationships of integral membrane proteins. One position
(funded by NIH) will focus on the transport mechanism of hydrophobic compounds
across the bacterial outer membrane as mediated by FadL-family proteins. The
Hi folks
If you've recently downloaded a pre-built copy of Mosflm version 7.0.1 for
Intel Mac (including the universal binary) and been surprised by the need
for libgfortran.1.dylib, read on. Otherwise, feel free to ignore this!
It seems my attempts to produce a statically linked OS X executa
Dear Harry,
Sorry, this did end up sounding harsher than I intended, and it could
have done with a few judiciously placed smileys :) . My mailer may also have
been overzealous: there was no intention of bombarding you with disapproval.
I was simply trying to say that we are still far f
Hi Bernhard,
Type: centrosymmetric rubredoxin
in google and you'll get a few papers including what I think was the
original work by Zawadzke & Berg.
Bart
Zawadzke LE, Berg JM.
Related Articles, Links
AbstractThe structure of a centrosymmetric protein crystal.
Proteins. 1993 Jul;16(
Dear Crystallographers,
Here are a few paradoxes about diffraction I would like to get some
answers about:
1. In every description of Braggs' law I've seen, the in-coming waves
have to be in phase. Why is that? Given that the sources used for
diffraction studies are mostly non-coherent.
2. Trying
My group has several vacancies to fill immediately: a Team Leader for
Infrastructure and Methods Development; two postdoc positions; and a
technician. This is the Protein Crystallography group of the
Structural Genomics Consortium, Oxford.
For details, please see respectively:
Team Leader:
On Friday 24 August 2007 12:22, Michel Fodje wrote:
> 1. In every description of Braggs' law I've seen, the in-coming waves
> have to be in phase. Why is that? Given that the sources used for
> diffraction studies are mostly non-coherent.
Think of Bragg's Law as explaining what happens to a singl
Michel Fodje wrote:
Dear Crystallographers,
Here are a few paradoxes about diffraction I would like to get some
answers about:
...
3. What happens to the photon energy when waves destructively interfere
as mentioned in the text books. Doesn't 'destructive interference'
appear to violate the f
> > 1. In every description of Braggs' law I've seen, the in-coming waves
> > have to be in phase. Why is that? Given that the sources used for
> > diffraction studies are mostly non-coherent.
>
> Think of Bragg's Law as explaining what happens to a single photon
> that is probabilistically scatte
> For every direction where there is destructive interference and a
> loss of energy there is a direction where there is constructive
> interference that piles up energy. If you integrate over all
directions
> energy is conserved.
For the total integrated energy to be conserved, energy will have
> You are just using the coherent fraction of the beam.
My point is that Braggs' law as currently understood does not preclude
the diffraction from waves which were non-coherent before hitting the
sample
> It is not clear at all how you arrive to that condition. By definition, if
> two waves are n
>For the total integrated energy to be conserved, energy will have to be
>created in certain directions to compensate for the loss in other
>directions. So in a direction in which the condition is met, the total
>will have to be more than the sum of the waves in that direction.
>How about consider
On Fri, 24 Aug 2007 14:40:13 -0600
Michel Fodje <[EMAIL PROTECTED]> wrote:
The mathematics works but doesn't necessarily mean the current
interpretation of the mathematics has any resemblance to what actually
happens in reality.
Sure, it does. Crystallography is traditionally
Michel Fodje wrote:
For every direction where there is destructive interference and a
loss of energy there is a direction where there is constructive
interference that piles up energy. If you integrate over all directions
energy is conserved.
For the total integrated energy to be conserved, en
Here's a fun way to think of it:
A photon hits a crystal and will diffract off in a certain direction
with the same energy as the original photon. The direction is subject to
a probability distribution based on the lattice, with angles at the
diffraction conditions being most likely and the br
Without resorting to a circular argument? You are asking too much.
However, this probability distribution is perfectly described by
considering a component wave model wherein coherence of the component
waves correlates with peaks in the probability distribution--i.e.
Bragg's Law.
IANAM (I am
Would it be taking it too far to suggest that one could go all the way
and consider that each electron diffracts not as groups in a plane but
as individual electrons and a photon impinging on an electron with with
a specific phase will be diffracted in a specific direction. However the
lattice arra
Dear All,
I am working with a protein that requires 10% glycerol throughout the
purification to keep it soluble. I have been very worried that having
glycerol in my protein solution when I am trying to crystallize it will
prevent me from obtaining crystals. I am curious to see if others have
succes
We've grown crystals of the cytochrome bc1 complex in the
presence of glycerol.
I think as high as 25% in the initial droplet (protein in 50%
glycerol mixed with equal volume of precipitant),
but that was diluted somewhat by reverse vapor diffusion.
Glycerol tends to increase the solubility in ou
The "Bragg planes" are a contrivance of our invention to make the
math simpler and allow us to converse in shorthand terms like "Bragg's
Law". The photon's wave function interacts with the wave functions
of every electron it overlaps with, which is many unit cells because
our photons have quit
We have crystallised many things with 10% Glycerol. If % is high enough, there
is also often the added bonus in that the crystals are naturally cryoprotected!
J
Edward Berry <[EMAIL PROTECTED]> wrote:>
> We've grown crystals of the cytochrome bc1 complex in the
> presence of glycerol.
>
> I t
On several occasions we've had to use 5-10% glycerol in the protein.
Remember to add the same to all your screens since otherwise the vapor
diffusion often works 'backwards' (i.e. the drops get fatter with time).
Artem
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED]
I have crystallized a refolded membrane protein in presence of Glycerol. It
did not seem to affect
crystallizability and speed of crystallization.
If you have no luck in presence of glycerol, try to lower the glycerol
concentration without
compromising on the stability of the protein (buffer e
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